Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma

Head and neck squamous cell carcinoma (HNSCC) includes a large subset of cancers that are driven by the human papilloma virus (HPV) and occur primarily in the oropharynx. Here, we use 10x single cell RNA-seq to profile 70,970 cells from 11 HPV-positive and 5 HPV-negative oropharyngeal tumors in order to uncover diversity in chromosomal aberrations, cellular states and viral gene expression between and within tumors. 16 tumors from treatment-naïve patients were dissociated after surgery and profiled by 10X. For three of the tumors, samples of normal tissue from the tumor margin were additionally profiled separately, and for one sample, a metastatic lymph node was separately profiled. Four samples had were FACS-sorted into CD45+ and CD45- fractions that were profiled separately. Of these, two were profiled using 10x 5'-sequencing. All other samples were profiled using 3' sequencing.